If bacteria were as powerful as nanotech, there would not be any need for nanotech. Nanotech could potentially be to bacteria what the space shuttle is to a horse.
Nanotech can neither replicate nor kill us yet. It's not magic, and evolution has a huge head start on dealing with issues like powering it and self-replication. Devices at that scale are, generally, quite frail to things like stray cosmic rays or other background radiation causing them to break down.
And the space shuttles are dead; there will be no more of them. Horses, meanwhile, have survived for millions of years, so you're making the opposite point by mistake.
